 Identifying linked genes:

 With completely unlinked genes, two genes are found on separate chromosomes and
approximately equal numbers of gametes are formed which contain either the parental
combinations of alleles (parental types) or a different combination of alleles (recombinant
types). However, genes for different characteristics which are found on the same chromosome
are linked.
 They are inherited, to a greater or lesser degree as if they were a single gene. When genes are
closely linked e.g. when they are located close to each other on a chromosome-then, when
gametes are formed, recombination events which separate them rarely occur during meiosis.
 If the genes are located further apart on the chromosome, the number of recombination events
in meiosis will be higher.
 Therefore, genes that are very close together are less likely to be split during the crossing over
stage of meiosis rather than genes that are further apart.
 If 2 or more genes are positioned very close together on a chromosome, they may be so tightly
linked that they are never split up during meiosis and the gametes formed will always be of the
parental types. If the genes are further apart, crossing over is more likely to occur, although the
majority of cases they will be passed on as a parental unit, sometimes they will be mixed and
recombinant gametes produced, which in turn will be reflected in offspring.
Interaction between loci: (Epistasis)
There are some cases where different loci interact to affect one phenotypic character.
In the inheritance of the feather colour in chicken, there is an interaction between the 2 gene
loci I/i and C/c.
Individuals carrying the dominant allele I, have white feathers even if they also carry the
dominant allele C, for colored feathers. Birds that are homozygous recessive are also white.
White leghorn chicken have the genotype IICC while white Wyandotte chicken have the
genotype iicc, a white leghorn is crossed with a white Wyandotte.

 Epistasis: When 2 different genes on different chromosomes affect the same feature. The alleles
of one gene affects the expression of another,
Parental phenotypes white white
Parental genotypes IICC iicc
Gametes IC ic
Offspring (F1)
genotypes all IiCc
Offspring phenotypes all white

These offspring are interbred to give another generation.

Parental phenotypes white white
Parental genotypes IiCc IiCc

Gametes IC or Ic or iC or ic IC or Ic or iC or ic
in equal proportions
Offspring (F2) genotypes and phenotypes:
Gametes from one parent
IC Ic iC ic
IICC IICc IiCC IiCc
IC
white white white white
Gametes IICc IIcc IiCc Iicc
Ic
from white white white white
other IiCC IiCc iiCC iiCc
parent iC
white white coloured coloured
IiCc Iicc iiCc iicc
ic
white white coloured white
The usual 9:3:3:1 ratio expected in this generation has been modified to 13 white: 3 colored
A different interaction is shown by the inheritance of flower color in salvia Pure breeding pink
flowered variety was crossed with a pure breeding white flowered variety. The offspring had
purple flower. Interbreeding these offspring resulted in purple, pink and white flowered plant in
a ratio 9:3:4.

Genotype Phenotype
A−B− purple
A−bb pink
aaB− white
aabb white
(− indicates that either allele of the gene may be present)
68
 Continuous and Discontinuous variation:

Discontinuous
1-Individuals show a limited number of distinct forms i.e.
with clear cut differences (qualitative differences)
2-There are no intermediates.
3-Not affected by environment.
4-Controlled by one/two genes. E.g. blood groups, ear
lobes, sex, wing length in drosophila, height in peas, sickle
cell anemia & hemophilia.
-The different alleles of a single gene locus have large
effects on the phenotype.
-Different genes have quite different effects on the
phenotype
Continuous
1-Individuals in a population show a graduation from one
extreme to the other (quantitative differences)
2-There are many intermediates.
3-Affected by environment.
4-Controlled by many genes (polygenic) E.g. height in man,
body weight, sight.
-The different alleles at a single gene locus have small
effects on the phenotypes.
-Different genes have additive effect on the phenotype.
-A large number of genes may have a combined effect on a
phenotypic trait. so they are called polygenes.

 The graphs of continuous variation show the normal distribution curve, but in discontinuous
variation, it may be plotted as a bar chart (distinct groups), or as two separate groups and
there is a normal distribution within each group, but between which there is no overlap.

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 Controlling gene expression:
 Every cell contains around 20000-25000 individual genes on the chromosomes, but in a
differentiated cell, between 10000 & 20000 of those genes are actively expressed.
 Different combinations are expressed in different cells creating variety of structure and function
in cells of different tissues.
 The expression of a gene involves two key stages:
a- Transcription from DNA to messenger RNA (mRNA)
b- Translation from mRNA to proteins.
 The different proteins in a cell and its quantities determine the type of cell and its function in the
body also the proteins can be changed once they have been synthesized giving another level of
control over gene expression.
 Transcription factors and the control of gene expression:
 Controlling gene expression happens by switching on/off the transcription of certain genes, using
a single mRNA molecule many proteins can be produced at a ribosome or a polysome.
 Transcription factors are proteins that bind to specific regions on DNA known as promoter
sequences affecting the process of transcribing the genetic material.
 Some transcription factors stimulate the transcription of a region of DNA by binding its
corresponding DNA promoter sequence.
 Other transcription factors bind to regions known as enhancer sequences that cause changes in
the structure of the chromatin making it more or less open to RNA polymerase.
 An open chromatin is associated with active gene
expression while closed chromatin is associated with
gene inactivity.
 Several different transcription factors will be involved
in the expression of a single gene, and a single
transcription factor may control the activity of several
genes giving the control over expressing or repressing
genes at different stages of development of the
organism in different cell types under different
circumstances in the body.

 RNA splicing:
 The mRNA produced from the transcription of DNA is
including the exons & introns (Non-Coding DNA). So
the mRNA produced is not quite finished when it is first
transcribed and its referred to as pre-mRNA.
 The modifications of pre-mRNA involve the removal of
introns and in some cases the exons.
 Enzyme complexes known as spliceosomes join
together the exons that are to be transcribed and
produce mature and functional mRNA.

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 The spliceosomes may join the same exons in a variety of ways in a process known as RNA splicing,
resulting in a single gene producing several versions of functional mRNA which is transcribed from
the same section of DNA.
 These different mRNA versions code for different amino acids arrangements producing different
polypeptides and proteins. So a single gene can produce several different phenotypes.
 This is one of the ways in which the genotype can produce more proteins than there are genes.

 Post translational control:

 Further modifications to proteins may occur after they have been synthesized, the protein may
remain intact or shortened or lengthened by enzymes to give variety of other proteins.
 Epigenetics:
 It studies genetic control by factors other than base sequences on DNA, one form of epigenetics
is the RNA splicing as it changes the mRNA and proteins produced from the original genetic code
 The phenotype of an organism is the result of combination of genetic information and they
environment in which they grow & develop such as UV levels and diet.
 Three intracellular systems can interact to control genes in response to environmental factors
including: DNA Methylation, Histone modification & Non-coding mRNA.
A. DNA Methylation:
 It is the addition of methyl group (CH3) at the site where
cytosine occurs next to guanine in the DNA chain with a
phosphate bond between them. The methyl group is added
by an enzyme called DNA Methyltransferase.
 DNA Methylation always silences a gene or a sequence of
genes; it changes the arrangement of the DNA molecule
and prevents transcription from taking place.
 DNA methylation is important in controlling gene
expression and has a major role in many processes including embryonic development and X
chromosome inactivation.
 In many specialized cells, many genes are silenced by DNA methylation most or all the time.
 DNA Demethylation is the removal of the methyl group enabling genes to be activated so they
can be transcribed.
 Problems with methylation and demethylation are associated with diseases, including number of
human cancers.

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B. Histone modification:
 Histones are positively charged proteins, in which DNA helices wind around to form chromatin.
 The histones determine the structure of the chromatin. When the chromatin is densely
supercoiled and condensed the genes are not available to be copied to make proteins and it is
called heterochromatin.
 Active chromatin is more loosely held together, with uncoiled regions of DNA making more genes
available for transcription so that new proteins can be made, producing cells of different types.
 Different factors are responsible for histones modification including steroid hormones.
Modifications of histones include the following:
I. Histone acetylation: It is the addition of acetyl group (-COCH3) to one of the lysines in the
histone structure. The addition of acetyl group opens up the structure and activates the
chromatin, allowing genes in this area to be transcribed, and removing the acetyl group
produces heterochromatin again.
II. Histone methylation: It is the addition of methyl group (-CH3) to a lysine in the histone.
Methylation can cause inactivation of the DNA or activation of a region depending on the
position of the methylated lysine.
Histone methylation plays a role in the silencing of one of the X chromosomes in every cell in
female mammals.
C. Non-Coding mRNA:
 About 90% of the human genome is transcribed into mRNA, but only 2% of those RNA molecules
code for proteins, the rest of the non-coding mRNA (ncRNA0 affect the transcription of the DNA
code or modifies the products of transcription.
 Genes and whole chromosomes can be silenced by ncRNAs, in female mammals one of the X
chromosomes in every cell is inactivated at random due to the presence of an ncRNA called X-
inactive specific transcript (Xist) which is produced by the active Xist gene on the inactive
chromosome.
 The ncRNA coats one of the X chromosomes in female calls and deactivates it, the chromosome
supercoils and condenses to form the stable, inactive Barr body.
 One X chromosome is inactivated in order to maintain the balance of gene products in males , XY
and females XX, Another role for ncRNA in epigenetics in chromatin modification where it acts on
histones to make areas of the DNA available or unavailable for transcription
 Cell differentiation:
 Cell differentiation occurs when unspecialized cells switch different genes on and off needed to
become specialized cells.
 Epigenetic modifications of the genetic material are responsible for these changes as they ensure
that a wide range of very specific proteins are made within the cell as it differentiates for a specific
function.
 The modification is often a result of DNA methylation or demethylation or histone modification and
these modifications maybe in response to internal stimuli from the cell itself or to changes outside
the cell (external stimulus)
 The process of cell differentiation can be summarized as follows:

35
a. Chemical stimulus (E.g demethylation) / Transcription factors
b. Certain genes are activated
c. mRNA produced from these genes
d. Translation of mRNA to polypeptide/protein
e. Permanent modification of the cell.

36
 Cell wall:
 It is a rigid structure which provides support to the cell and keeps its shape, It is made of
cellulose.
 Suberin is added to the cell wall in cork tissues & lignin is part of cell wall structure in wood.
These compounds reduce the permeability of the cell wall, so water & dissolved substances can’t
pass through it.
 The plant cell wall consists of several layers. The middle lamella is the first layer & is made when
the plant cell divides into 2 new cells. It is made of pectin that binds with calcium ions to form
calcium pectate which binds to cellulose on either side. The wall made at first is flexible & all
cellulose microfibrils are arranged in a similar direction. They are called primary cell wall.
 Secondary thickening may occur as the plant ages. A secondary cell wall builds up with the
cellulose microfibrils laid at different angles to each other, this makes the material more rigid.
Hemi-cellulose help to harden it further. Secondary cell wall may contain extra substances as
lignin. Secondary cell wall is present in tissues like xylem & sclerenchyma.
 Cellulose is a polysaccharide made up of β cellulose joined together, while starch is a
polysaccharide made up of α-glucose.
 A condensation reaction between the –OH group on the first carbon of one glucose and the –OH
on the fourth carbon of the adjacent glucose links the two glucose molecules. A 1,4 glycosidic
bond forms. In cellulose, all the glycosidic bonds are 1,4; there are none of the 1,6 glycosidic
bonds that occur in starch. Because of this, cellulose is a long unbranched molecule.

39
 Each cellulose chain typically contains between 1000 and 10 000 glucose units. Unlike an
amylose molecule that winds into a spiral shape, the cellulose molecules remain as straight
chains. Hydrogen bonds form between the –OH groups in neighboring cellulose chains, forming
bundles called microfibrils. Individually, the hydrogen bonds are relatively weak compared with
the glycosidic bonds, but together the large number of hydrogen bonds in the microfibril
producing a strong structure
  Sustainability: It means using material that can be replaced and available for future generations.
Plants are vital in developing sustainable resources. People are realizing that natural plant fibres
are much more sustainable for a range of uses e.g. clothing fabrics, ropes and insulating material.

 Bioplastics:
 Most plastics such as polyethene & PVC are synthetic polymers, made from petrochemicals
originating from oil which is a non-renewable resource. These plastics are non-biodegradable
which has lead to plastic pollution.
 Types of bioplastics:
1. Cellulose based plastics, made from wood pulp, used to make plastic wrapping for food such
as cellophane.
2. Thermoplastic starch (made of starch and gelatin) is used to make capsules to contain drugs.
They are smooth, absorb water and easily swallowed.
3. Polylactic acid (PLA) has similar properties to polyethene, but is biodegradable. It is used to
make computer casing, mobile phones and drinking cups.
4. Poly-3-hydroxybutyrate (PHB) which is used in care parts and in bank notes.
 When plastics are broken down by decomposers they can produce methane which is a
greenhouse gas, so they can be damaging to the environment.
 Bioplastics are still much more expensive than the oil based alternatives, because the technology
is still very new.
 Minerals needed by plants:
1- Calcium: found in the middle lamella of plant cells, combines with pectin to form calcium
pectate which holds plant cells together.
 Deficiency in calcium causes growing points to die and young leaves become yellow.
2- Magnesium: Needed to make the green pigment chlorophyll, also needed for the formation of
enzymes needed for nucleic acid synthesis.
 Deficiency in magnesium causes yellow areas on the leaf and decreases growth rate of
plants.
3- Nitrates: Needed to make amino acids and therefore proteins such as enzymes and other
proteins needed for growth, DNA & hormones.
 Deficiency in nitrates causes stunted growth and yellowing of leaves.
4- Phosphates: Needed for the formation of ATP and synthesis of nucleic acids
 Deficiency in phosphates causes purple spots on the leaves and poor growth

46
 Uses of plant fibers:
 Plant fibers are used to make ropes, papers & cloth but the fibers must be extracted from the
plants first.
 The fibers are long sclerenchyma fibers & xylem tissues which are very tough.
 Fibers have great tensile strength which means that they cannot be easily broken by pulling
making them useful.
 Bundles of fibers are much stronger than individual ones.
 Plant fibers have also become source materials for plastics, and as a source of power & fuel .
 The use of plant fibers and starch is better than using oil based products and plastics because
they are sustainable resources, available to next generations & biodegradable which can be
acted upon by enzymes and don’t cause pollution.
 Plant fibers tensile strength can be measured by measuring the maximum weight that fibers can
withstand before breaking the fibers

 Plant based medicines:

 The plants have ways of protecting themselves against microbial attack, they produce chemicals.
 Defenses can include both antiseptic compounds & antibiotics e.g. cotton plants produce a
phenol called gossypol which is an antiseptic which kills bacteria that might attack the seed.
 Some plants and fungi have antimicrobial properties, other produce compounds that have effects
like pain relief and destroying cancer cells. The scientists discovered that the active ingredient in
the bark was salicylic acid where they developed a method to extract & purify it to form aspirin.
 One of the advantages of extracting and purifying the beneficial drugs found in plants is that it is
possible to give known, repeatable doses of the active ingredient.
 The levels of a chemical in any part of the plant will vary with age of the plant, season of the year
& even the time of the day. By extracting the chemicals & purifying them, an extract dose can be
achieved every time.
 Parts of the world which could not develop because of the high prevalence of the diseases are
now developing due to the benefits of plant-based medicines. E.g. Quinine which comes from
cinchona tree is used to prevent & treat malaria. The use of this drug made it possible for loggers
and developers to work in many malarial areas.

47
 Bacterial growth:
 To investigate bacteria for scientific experiments for example or to investigate potential
medicines, we need to culture them. This involves growing large number of bacteria, they need
to be given the correct level of nutrients and oxygen together with the ideal temperature and PH.
 The bacteria are often grown on agar plates/agar jelly which contains all the nutrients the
bacteria need to grow well.
 It’s important to take care when culturing microorganisms because:
1. Some of the cultured harmless strains may mutate & become pathogenic.
2. There’s a risk of contamination by pathogenic microorganisms from the environment.
3. Some other microorganisms from air or skin may contaminate the culture.
So we have to use aseptic techniques to keep everything sterile such as:
1. All the equipment & instruments must be sterile by using Bunsen burner flame.
2. All cultures should be disposed off safely by sealing them in plastic bags & sterilising them at
121oC for 15 minutes under pressure and throwing them.

 Contemporary drug testing:

A. Pre-clinical trials: Animal studies and laboratory studies on isolated cells and tissue cultures
assess safety and determine whether the compound is effective against the target disease.
These tests can take several years to complete. Thousands of chemicals go through pre-clinical
testing, but only handfuls are ever approved for clinical trials on humans.
B. Phase I: A small group of volunteers are told about the drug and given different doses. These
volunteers are normally healthy. The trial confirms whether or not the compound is being
absorbed, distributed, metabolized and excreted by the body in the way predicted by the
laboratory tests. The effects of different doses are monitored.

C. Phase II: Small groups of volunteer patients (100–300 people with the disease) are treated to
look at the drug’s effectiveness. If the results are promising, phase III trials are set up.

D. Phase III: A large group of patients (1000–3000 people) is selected and divided randomly into
two groups. One group is given the compound being investigated. The second is given an
inactive compound known as a placebo. If there is an existing treatment for the disease, the
standard treatment is given rather than a placebo. It is important that neither the patients nor
the doctors know who is having the compound under investigation and who is having the
placebo or standard treatment. This is known as a double-blind trial. If the compound being
investigated is effective, then the results will show a statistically significant improvement in the
patients receiving the treatment compared with patients given the placebo or standard

treatment. The tests also look for any adverse reactions in the patients.

49
 Concept of species:
 Adaptations within a species and species numbers are used to monitor the effect of both
natural environmental changes and changes that result from human activity. Species are
defined in many ways:
1. Morphological species concept:
 Morphological species model is based on appearance of organism.
 Scientists in this model look at the outer & inner morphology and group them into Genus,
Species…etc according to the extent of difference or similarity of the physical
characteristics.
 However, the appearance of an organism can be affected by many different things and
there can be a huge amount of variation within a group of closely related organisms. In
organisms that show sexual dimorphism, in which there’s a great deal of difference
between the male and female, the different sexes could be confused as different species in
a morphological species model.

2. The reproductive or biological species concept:

 A model of a species based on reproductive behaviour.
 Species according to this model is defined as a group of organisms with similar
characteristics that interbreed to produce fertile offspring.
 This definition has limitations in that all organisms in a species can’t interbreed to produce
fertile offspring because they don’t live in the same area. So populations of organisms of
the same species may not interbreed because they are in different places and not because
they are different species.
 In this model, if individual from different populations mate, they are considered the same
species if fertile offspring are produced and genes are combined from parents to offspring.
E.g. horses and donkey look similar and can interbreed but they produce a mule which is
infertile and genes can’t flow to next generations, so they are considered different species.
Other organisms like lions and tigers are different species but they interbreed to produce
fertile offspring. To overcome limitations with this model, 2 more definitions of species
based on reproductive capability are:
A. A group of organisms with similar characteristics that are all potentially capable of
breeding to produce fertile offspring.
B. A group of organisms in which genes can flow between individuals.

52
 Molecular Phylogeny:
 The analysis of structure of different chemicals e.g. proteins (as blood pigments) and DNA to
identify relationships between groups of organisms is called molecular phylogeny.
 These evidences may support of conflict with relationships based on morphology.
 Identification of patterns in DNA and RNA of different individuals & between different species,
also comparison between amino acids sequences of similar protein between different species

has many implications as species identification and development of models of the relationships
between organisms over time.
 Gel electrophoresis is the technique used to identify patterns, which is a variation of
chromatography used to separate DNA & RNA fragments, proteins and amino acids according to
their size and charge.
 A combination of DNA analysis, protein analysis and anatomical observations can bring some
relationships to light.
 One way of showing relationships between different groups is the Phylogenic tree which is a
model of how different organisms are related.
 A phylogenic tree shows common ancestor which may no longer exist and the tree branches as
different species appear as a result of natural selection.
 Some scientists think that chloroplasts became part of “Eukaryotic ancestor” cells first; other
think that mitochondria were the first endosymbionts.
 The analysis of structures of different chemicals and genes to identify the inter-relationships
between groups of organisms.
 It’s clear that eukaryotic cells have evolved from prokaryotic cells
 later some scientists discovered by molecular phylogeny that there are 3 domains, 2 prokaryotic
domains which are Bacteria and Archaea (both are prokaryotic) and the Eukaryota
 The three groups are said to have a single common ancestor.
 Some evidences have shown that Archaea are more closely related to Eukaryota than to bacteria.

54
 Archaea replicate by binary fission which is controlled within a cell cycle, which is similar to the
cell cycle of Eukaryotic cells but different from replication in bacterial cells.
 Membrane structures and proteins are unique in Archaea and different from bacteria and
Eukaryotes
 The Archaea have an ester link in their lipids, giving branched molecules that provides extra
strength in extreme environment. This supports a model which suggests a different origin for
some cells in Archaea and bacterial systems, but shows Eukaryotes combining features of the
both.
 Research in this field are published in peer reviewed journals so that other scientists can repeat
procedures to verify the results

55
  Population bottlenecks:
 A large population is needed to maintain large and diverse gene pool. Even with a large
population, allele frequencies are affected by factors such as mutations & non-random
mating. If the size of the population is greatly reduced so is the gene pool and allele
frequency.
 An environmental disaster can reduce the size of a population rapidly such as new disease,
predators or human hunting. This is called population bottleneck and it causes severe
decrease in the gene pool of a population and dramatic change in the allele frequency and
genetic diversity.
 After a catastrophic event the remaining population is vulnerable to complete loss of some
alleles and a single mutation can have bigger effect than usual. As the population recovers, it
may become different from the original population genetically that it becomes a new
species.

 The founder effect:

 It is the loss of genetic variation that
occurs when a small number of individuals
leave the main population and set up a
separate new population, producing a
voluntary population bottleneck.
 The alleles carried by the individuals who
leave the main population are unlikely to
include all the alleles or the same
frequencies as the original population.
 Any unusual genes in the founder
members of the new population may
become more frequent as the population
grows.

 Sustainability:
 Habitats and ecosystems can be conserved with less conflict by encouraging sustainable
methods of land use.
 For example, illegal logging operations in rainforest cut down all trees and burn the ground
afterwards to harvest wood to sell and clear the soil for farming. The soil is soon exhausted
and biodiversity lost.
 If we harvest the trees selectively and replant for the future, biodiversity can be maintained
while people continue to use the forest for income. This is sustainable forestry.
 Sustainable agriculture includes farming methods that minimize damage to the environment
and avoid monocultures.
 They involve using organic fertilizers and minimizing the usage of artificial fertilizers and
chemical pesticides, using biological pest control.
 Large-scale farming is vital to provide the food we need but often using sustainable methods
such as biological pest control can increase the yield and improve profits while being cheaper
and better for the environment.
 Tourism can also be developed in a sustainable way by providing jobs and money for local
people while conserving the environment.